Abstract

Background

The oil palm (Elaeis guineensis Jacq.) is a perennial monocotyledonous tropical crop species that is now the world's
number one source of edible vegetable oil, and the richest dietary source of provitamin
A. While new elite genotypes from traditional breeding programs provide steady yield
increases, the long selection cycle (10-12 years) and the large areas required to
cultivate oil palm make genetic improvement slow and labor intensive. Molecular breeding
programs have the potential to make significant impacts on the rate of genetic improvement
but the limited molecular resources, in particular the lack of molecular markers for
agronomic traits of interest, restrict the application of molecular breeding schemes
for oil palm.

Results

In the current study, 6,103 non-redundant ESTs derived from cDNA libraries of developing
vegetative and reproductive tissues were annotated and searched for simple sequence
repeats (SSRs). Primer pairs from sequences flanking 289 EST-SSRs were tested to detect
polymorphisms in elite breeding parents and their crosses. 230 of these amplified
PCR products, 88 of which were polymorphic within the breeding material tested. A
detailed analysis and annotation of the EST-SSRs revealed the locations of the polymorphisms
within the transcripts, and that the main functional category was related to transcription
and post-transcriptional regulation. Indeed, SSR polymorphisms were found in sequences
encoding AP2-like, bZIP, zinc finger, MADS-box, and NAC-like transcription factors
in addition to other transcriptional regulatory proteins and several RNA interacting
proteins.

Conclusions

The identification of new EST-SSRs that detect polymorphisms in elite breeding material
provides tools for molecular breeding strategies. The identification of SSRs within
transcripts, in particular those that encode proteins involved in transcriptional
and post-transcriptional regulation, will allow insight into the functional roles
of these proteins by studying the phenotypic traits that cosegregate with these markers.
Finally, the oil palm EST-SSRs derived from vegetative and reproductive development
will be useful for studies on the evolution of the functional diversity within the
palm family.